Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa

1997 ◽  
Vol 75 (12) ◽  
pp. 2045-2056 ◽  
Author(s):  
Dominik Begerow ◽  
Robert Bauer ◽  
Franz Oberwinkler
Keyword(s):  
Molecular Phylogeny ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
The Other ◽  
Lsu Rdna ◽  
Smut Fungi ◽  
Neighbor Joining ◽  
Phylogenetic Studies ◽  
Key Words Basidiomycete

To show phylogenetic relationships among the smut fungi and their relatives, we sequenced a part of the nuclear LSU rDNA from 43 different species of smut fungi and related taxa. Our data were combined with the existing sequences of seven further smut fungi and 17 other basidiomycetes. Two sets of sequences were analyzed. The first set with a representative number of simple septate basidiomycetes, complex septate basidiomycetes, and smut fungi was analyzed with the neighbor-joining method to estimate the general topology of the basidiomycetes phylogeny and the positions of the smut fungi. The tripartite subclassification of the basidiomycetes into the Urediniomycetes, Ustilaginomycetes, and Hymenomycetes was confirmed and two groups of smut fungi appeared. The smut genera Aurantiosporium, Microbotryum, Fulvisporium, and Ustilentyloma are members of the Urediniomycetes, whereas the other smut species tested are members of the Ustilaginomycetes with Entorrhiza as a basal taxon. The second set of 46 Ustilaginomycetes was analyzed using the neighbor-joining and the maximum parsimony methods to show the inner topology of the Ustilaginomycetes. The results indicated three major lineages among Ustilaginomycetes corresponding to the Entorrhizomycetidae, Exobasidiomycetidae, and Ustilaginomycetidae. The Entorrhizomycetidae are represented by Entorrhiza species. The Ustilaginomycetidae contain at least two groups, the Urocystales and Ustilaginales. The Exobasidiomycetidae include five orders, i.e., Doassansiales, Entylomatales, Exobasidiales, Georgefischeriales, and Tilletiales, and Graphiola phoenicis and Microstroma juglandis. Our results support a classification mainly based on ultrastructure. The description of the Glomosporiaceae is emended. The Doassansiopsaceae, Melanotaeniaceae, and Urocystaceae are proposed as new taxa. Key words: basidiomycete systematics, LSU rDNA, Microbotryales, molecular phylogeny, smut fungi, Ustilaginomycetes.

Phylogeny of the rust fungi: an approach using nuclear large subunit ribosomal DNA sequences

2003 ◽  
Vol 81 (1) ◽  
pp. 12-23 ◽  
Author(s):  
Wolfgang Maier ◽  
Dominik Begerow ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Rust Fungi ◽  
Monophyletic Group ◽  
Neighbor Joining ◽  
Natural Group ◽  
Outgroup Species ◽  
Large Subunit Rdna

Sequence data from nuclear large subunit ribosomal DNA was used to infer phylogenetic relationships of selected genera of the Uredinales. We investigated 52 rust fungi representing nine families and three outgroup species. Neighbor joining analysis and a Bayesian method of phylogenetic inference using Monte Carlo Markov chains confirm the rust fungi as a natural group and indicate that Puccinia, Uromyces, Endophyllum, and Cumminsiella have a common origin. The autoecious Rosaceae-rusts Phragmidium, Kuehneola, Triphragmium, and Trachyspora are a monophyletic group. The gasteroid genus Ochropsora is closely related to Tranzschelia. While the Pucciniastreae sensu Dietel (1938) is recognized as a monophyletic group in neighbor joining analysis, the Pucciniaceae s.l. (Dietel 1928) is supported by Bayesian analysis. The following genera appear to be monophyletic: Chrysomyxa, Coleosporium, Cronartium, Gymnosporangium, Melampsora, Phragmidium, and Tranzschelia, whereas the genera Puccinia, Pucciniastrum, Thekopsora, and Uromyces are not.Key words: molecular phylogeny, systematics, nuclear large subunit rDNA, Basidiomycota, Urediniomycetes, Uredinales.

Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit ribosomal DNA sequences

1999 ◽  
Vol 77 (12) ◽  
pp. 1790-1800 ◽  
Author(s):  
Ale×andra Riethmüller ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Phylogenetic Studies

scholarly journals Taxonomic relationships in the genus <i>Ammonia</i> (Foraminifera) based on ribosomal DNA sequences

2000 ◽  
Vol 19 (1) ◽  
pp. 85-95 ◽  
Author(s):  
Maria Holzmann ◽  
Jan Pawlowski
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Morphological Variability ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Taxonomic Relationships ◽  
Rdna Sequences ◽  
Ecological Features ◽  
Genotypic Group

Abstract. The genus Ammonia is a common benthic foraminifer which is widely distributed in nearshore marine environments. Its large morphological variability causes considerable difficulties in species identification. In the present study, we investigated taxonomic relationships in Ammonia by using a molecular approach based on ribosomal DNA sequences. We obtained 149 partial large subunit ribosomal DNA (LSU rDNA) sequences and 23 small subunit ribosomal DNA (SSU rDNA) sequences from 88 living Ammonia specimens which were collected from free-living populations in 14 localities. Sequence analysis revealed the presence of eight distinct genotypic groups (T1–T7, T9) and one distinct genotype that is represented by one specimen (T8). Examination of morphological characters shows that only one genotypic group can be clearly distinguished by its morphology. Biogeographical and ecological features are used for an additional characterization and it seems that the different groups live in relatively well defined environmental conditions and that only one genotypic group is cosmopolitan, while the others have a rather restricted geographical distribution. According to our study, three of the genotypic groups can be regarded as distinct species.

On the subdivision of Ceratocystis s.l., based on partial ribosomal DNA sequences

1993 ◽  
Vol 71 (1) ◽  
pp. 52-63 ◽  
Author(s):  
G. Hausner ◽  
J. Reid ◽  
G. R. Klassen
Keyword(s):  
Key Words ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Cell Walls ◽  
Large Subunit ◽  
Rdna Sequences

Analyses of partial rDNA sequences from both the small and large subunit genes of species of Ceratocystis s.l. support the contention that species that lack Chalara anamorphs, are resistant to cycloheximide, and have rhamnose in their cell walls should be assigned to Ophiostoma, whereas only species with Chalara anamorphs should be accommodated in Ceratocystis s.s. The data also show that Ceratocystiopsis is polyphyletic, and Sphaeronaemella fimicola appears to have little relation to either Ceratocystis or Ophiostoma. Key words: Ceratocystis, Ophiostoma, phylogeny, partial rDNA sequences.

scholarly journals Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Yi-Fan Cao ◽  
Hui-Xia Chen ◽  
Yang Li ◽  
Dang-Wei Zhou ◽  
Shi-Long Chen ◽  
...  
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Sister Relationship ◽  
Tibetan Antelope ◽  
A New Species

Abstract Background The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered species of mammal endemic to the Qinghai-Tibetan Plateau. Parasites and parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites of the Tibetan antelope remains limited. Methods Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens was observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences, i.e. small subunit ribosomal DNA (18S), large subunit ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 (cox1), were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox1 sequence data, respectively, in order to clarify the systematic status of these nematodes. Results Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum (Oxyurida: Oxyuridae). There was no intraspecific nucleotide variation between different individuals of S. longicaudatum n. sp. in the partial 18S, 28S, ITS and cox1 sequences. However, a high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results suggest that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, as it formed a sister relationship to the genus Oxyuris. Conclusions A new species of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) is described. Skrjabinema longicaudatum n. sp. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to the knowledge of the species diversity of parasites from the Tibetan antelope, and clarify the systematic position of the genus Skrjabinema.

Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit ribosomal DNA sequences

2000 ◽  
Vol 77 (12) ◽  
pp. 1790-1800 ◽  
Author(s):  
Alexandra Riethmüller ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Bootstrap Method ◽  
Large Subunit ◽  
Phytophthora Megasperma ◽  
Parsimony Method ◽  
Natural Group ◽  
Maximum Parsimony Method ◽  
Phylogenetic Studies ◽  
Main Emphasis

To reveal phylogenetic relationships within the Peronosporomycetes (Oomycetes), we sequenced a part of the nuclear rDNA coding for the ribosomal large subunit of 46 Peronosporomycetes species and one representative of the Xanthophyta. The main emphasis of our study was put on the phylogenetic relationships within the Saprolegniomycetidae. We supplemented our data with a sequence of Phytophthora megasperma Drechsler from GenBank. Two sets of sequences were analysed using the neighbor-joining method, statistically supported by the bootstrap method, as well as the maximum parsimony method. Our results are well compatible with the tripartite subclassification of the Peronosporomycetes into Saprolegniomycetidae, Rhipidiomycetidae and Peronosporomycetidae, as well as with the placement of the orders Saprolegniales and Leptomitales in the Saprolegniomycetidae. Pachymetra chaunorhiza Croft & Dick, which has been placed in the Sclerosporales, was grouped within the Saprolegniales. Within the Peronosporomycetidae, the orders Peronosporales and Pythiales could not be separated. There are indications that Phytophthora de Bary and the Peronosporales form a common natural group. The genus Achlya Nees proved to be a heterogeneous group.

scholarly journals Phylogenetic Relationships of Agaric Fungi Based on Nuclear Large Subunit Ribosomal DNA Sequences

2000 ◽  
Vol 49 (2) ◽  
pp. 278-305 ◽  
Author(s):  
Jean-Marc Moncalvo ◽  
François M. Lutzoni ◽  
Stephen A. Rehner ◽  
Jacqui Johnson ◽  
Rytas Vilgalys
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Large Subunit
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